Apoptosis, cell proliferation and in vivo biological behaviour of primary and metastatic tumour cells of an AKR lymphoma variant

The possibility that apoptosis and/or cell proliferation have a role in tumour progression in a murine T cell lymphoma was tested. The model consisted of the comparison of primary (PT) and metastatic tumour (MT) cells. The PT cells, but not the MT cells displayed a very pronounced tendency for spontaneous apoptosis. Proliferative capacity of MT cells was lower than that of PT cells, suggesting that it does not contribute to the metastatic phenotype in this system. Release from apoptosis does however, probably, play a role in the aggressiveness of the lymphoma.     

The Cenomanian of northern Germany: facies analysis of a transgressive biosedimentary system

A facies analysis of the epicontinental marine Cenomanian sediments of northern Germany shows the presence of 17 facies types (FTs, including several subtypes) which can be assigned to three facies associations: 1) an inner shelf facies association (FT 1–8) with high amounts of terrigenous material and/or high-energy depositional features, 2) a middle shelf facies association (FT 9–15) of predominantly calcareous sediments with moderate amounts of generally fine siliciclastics, and 3) an outer shelf facies association (FT 16–17) of low-energy, fine-grained, pure limestones. These three facies associations roughly correspond to the well-known lithological units of the Cenomanian of northern Germany, i.e., the Essen Greensand/Cenomanian Marls complex, the Pläner Limestones, and the Poor rhotomagense Limestones. The sediments were deposited on a northward-dipping homoclinal ramp with more-or-less shoreline-parallel facies belts. The sediment composition on this ramp-like shelf was a function of the varying importance of three different sediment sources: 1) terrigenous input from the south (Rhenobohemia), generally fining/decreasing in a proximal–distal (i.e., S–N) direction; 2) production of skeletal grains, mainly by macrobenthic organisms; and 3) settling of planktic carbonate (mainly calcispheres and calcareous nannofossils). In response to decreasing water energy with increasing water depth, the seaward decreasing terrigenous influence, and increasing planktic carbonate production, increasingly finer and more calcareous sediments were deposited in a proximal–distal transect. This rather straightforward picture was slightly modified by highest carbonate accumulation rates (planktic and benthic) on the middle shelf, forming a mid-shelf depocenter (fossiliferous, calcisphere-rich Pläner Limestones). Time-transgressive, southward-directed onlap of this biosedimentary system during the Cenomanian caused a significant retreat of the coastline towards the south and a retrogradational stacking of facies belts, explaining the broadly similar facies development and lithology of Cenomanian successions across northern Germany. The boundaries of the lithological units, however, tend to be considerably diachronous in a distal–proximal transect. In the late Middle and early Late Cenomanian, a final drowning and facies levelling (“oceanization”) is indicated by the widespread deposition of uniform calcareous nannofossil mudstones (Poor rhotomagense Limestones).     

The Advantage of Playing Home in NBA: Microscopic,Team-Specific and Evolving Features

The idea that the success rate of a team increases when playing home is broadly accepted and documented for a wide variety of sports. Investigations on the so-called “home advantage phenomenon” date back to the 70’s and ever since has attracted the attention of scholars and sport enthusiasts. These studies have been mainly focused on identifying the phenomenon and trying to correlate it with external factors such as crowd noise and referee bias. Much less is known about the effects of home advantage in the “microscopic” dynamics of the game (within the game) or possible team-specific and evolving features of this phenomenon. Here we present a detailed study of these previous features in the National Basketball Association (NBA). By analyzing play-by-play events of more than sixteen thousand games that span thirteen NBA seasons, we have found that home advantage affects the microscopic dynamics of the game by increasing the scoring rates and decreasing the time intervals between scores of teams playing home. We verified that these two features are different among the NBA teams, for instance, the scoring rate of the Cleveland Cavaliers team is increased ≈0.16 points per minute (on average the seasons 2004–05 to 2013–14) when playing home, whereas for the New Jersey Nets (now the Brooklyn Nets) this rate increases in only ≈0.04 points per minute. We further observed that these microscopic features have evolved over time in a non-trivial manner when analyzing the results team-by-team. However, after averaging over all teams some regularities emerge; in particular, we noticed that the average differences in the scoring rates and in the characteristic times (related to the time intervals between scores) have slightly decreased over time, suggesting a weakening of the phenomenon. This study thus adds evidence of the home advantage phenomenon and contributes to a deeper understanding of this effect over the course of games.     

Quantification of hydrolyzed peptides and proteins by amino acid fluorescence

Reliable quantification of peptides and proteins is essential for drug discovery. We report the successful development and validation of an accurate and broadly applicable high performance liquid chromatography hyphenated to fluorescence detector procedure for the quantitative determination of the aromatic amino acids tyrosine, phenylalanine, and tryptophan, without relying on derivatization chemistry. Using ion‐pair chromatography, fluorescent amino acids were clearly separated within 10 minutes. The hydrolysis of peptides was performed under acidic and heated conditions to yield the monomeric building blocks. Various protecting agents were tested to ensure tryptophan stability. The presented analytical method accurately (>95%) quantifies all fluorescent residues. The power of the method was confirmed by correct quantification of protein reference standard to 98.6% over all fluorescence traces. The method allowed us to identify pre‐analytical differences between the nominal and actual concentrations of 12 peptide solutions. Salt formation, weighing errors, and other pre‐analytical pitfalls resulted in noteworthy differences of up to 85% between the indicated and actual concentration of peptide solutions, subsequently leading to false positive or negative interpretation of activity data. Finally, only one solution is needed to perform quantification as well as UV‐purity tests and can further be used as stock solution for activity testing.     

A generalized kinetic model for the study of microbial growth

The following general equation is proposed to represent the kinetics of microbial growth \documentclass{article}\pagestyle{empty}\begin{document}$$\phi (dR/dt) + \psi R + X = 0$$\end{document}, where phi and psi depend on several parameters of the fermenting system. The values of phi and psi were calculated based on results obtained in a batch lactic acid fermentation, a batch cultivation of yeast on diesel oil, and a continuous cultivation of yeast on sugarcane molasses.     

Hollow fiber-based liquid phase microextraction with factorial design optimization and gas chromatography–tandem mass spectrometry for determination of cannabinoids in human hair

A new method, based on hollow fiber liquid-phase microextraction (HF-LPME) and gas chromatography–tandem mass spectrometry (GC–MSMS), was developed for determination of Δ⁹-tetrahydrocannabinol (THC), cannabidiol (CBD) and cannabinol (CBN) in samples of human hair. Since hair is a solid matrix, the samples were subjected to alkaline digestion using NaOH. The aqueous solutions obtained were extracted using a 6 cm polypropylene fiber (600 μm i.d., 200 μm wall thickness, 0.2 μm pore size) for each extraction. A 2⁵⁻¹ fractional factorial design for screening, and a central composite design for optimization of significant variables, was applied during development of the extraction method. The variables evaluated were the type of extraction solvent, pH, stirring speed, extraction time, and acceptor phase volume. The optimized conditions for the proposed extraction procedure were 10 mg of hair sample; 20 μL of butyl acetate; aqueous (pH 14) donor phase containing 6.8% NaCl; 600 rpm stirring speed; 20 min extraction time. A linear response was obtained in the ranges 1–500 pg mg⁻¹ (CBD and CBN) and 20–500 pg mg⁻¹ (THC), with regression coefficients >0.99. Precision, determined as the relative standard deviation, was 3.3–8.9% (intra-day) and 4.4–13.7% (inter-day). Absolute recoveries varied in the ranges 4.4–4.8% (CBD), 7.6–8.9% (THC) and 7.7–8.2% (CBN). Limits of detection (LOD, S/N = 3) and quantification (LOQ, S/N = 10) were 0.5–15 pg mg⁻¹ and 1–20 pg mg⁻¹, respectively. The method was successfully used to determine CBD, THC and CBN in hair samples from patients in a drug dependency rehabilitation center. Concentrations varied in the ranges 1–18 pg mg⁻¹ (CBD), 20–232 pg mg⁻¹ (THC) and 9–107 pg mg⁻¹ (CBN), confirming the suitability of the method for monitoring studies.     

An Unusual ERAD-Like Complex Is Targeted to the Apicoplast of Plasmodium falciparum

Many apicomplexan parasites, including Plasmodium falciparum, harbor a so-called apicoplast, a complex plastid of red algal origin which was gained by a secondary endosymbiotic event. The exact molecular mechanisms directing the transport of nuclear-encoded proteins to the apicoplast of P. falciparum are not well understood. Recently, in silico analyses revealed a second copy of proteins homologous to components of the endoplasmic reticulum (ER)-associated protein degradation (ERAD) system in organisms with secondary plastids, including the malaria parasite P. falciparum. These proteins are predicted to be endowed with an apicoplast targeting signal and are suggested to play a role in the transport of nuclear-encoded proteins to the apicoplast. Here, we have studied components of this ERAD-derived putative preprotein translocon complex in malaria parasites. Using transfection technology coupled with fluorescence imaging techniques we can demonstrate that the N terminus of several ERAD-derived components targets green fluorescent protein to the apicoplast. Furthermore, we confirm that full-length PfsDer1-1 and PfsUba1 (homologues of yeast ERAD components) localize to the apicoplast, where PfsDer1-1 tightly associates with membranes. Conversely, PfhDer1-1 (a host-specific copy of the Der1-1 protein) localizes to the ER. Our data suggest that ERAD components have been “rewired” to provide a conduit for protein transport to the apicoplast. Our results are discussed in relation to the nature of the apicoplast protein transport machinery.The apicomplexan parasite Plasmodium falciparum is the etiological agent of malaria tropica, the most severe form of human malaria, responsible for over 250 million infections and 1 million deaths annually (61). Many apicomplexan parasites, including P. falciparum, harbor a so-called apicoplast, a complex plastid of red algal origin which was gained by a secondary endosymbiotic event (27, 58). Although during the course of evolution this plastid organelle has lost the ability to carry out photosynthesis, it is still the site of several important biochemical pathways, including isoprenoid and heme biosynthesis, and as such is essential for parasite survival (60). As in other plastids, the vast majority of genes originally encoded on the plastid genome have been transferred to the nucleus of the host. As a result, their gene products (predicted to constitute up to 10% of all nucleus-encoded proteins) must be imported back into the apicoplast (12). The apicoplast is surrounded by four membranes (55), and this protein import process thus represents a major cell biological challenge and has attracted much research interest, not least due to the importance of P. falciparum as a human pathogen (16, 50).The signals directing transport of nucleus-encoded proteins to complex plastids, including the apicomplexan apicoplast, have been studied in great detail in recent years, and reveal that such proteins are endowed with specific N-terminal targeting sequences, referred to as a bipartite topogenic signals (BTS), that direct their transport to this compartment (50). BTS are composed of an N-terminal endoplasmic reticulum (ER)-type signal sequence, which initially allows proteins to enter the secretory system via the Sec61 complex (59). Following this, proteins are carried via a Golgi complex-independent transport step to the second outermost membrane, from where they are then translocated across the remaining three apicoplast membranes, directed by the second part of the BTS, the transit peptide (51). Based on evolutionary considerations, it has long been suggested that transport across the inner two apicoplast membranes occurs via a Toc/Tic-like (where Toc and Tic are translocons of the outer and inner chloroplast envelopes, respectively) protein translocase machinery, and this is supported by a recent publication that provides evidence for an essential role of a Toxoplasma gondii Tic20 homologue in this transport process (50, 57). Despite this progress, it is still unclear how proteins travel across the second and third outer apicoplast membranes. Several models have been discussed to account for this transport step, including vesicular shuttle and translocon-based mechanisms (recently reviewed in reference 19), but until recently no actual molecular equipment had been found which could account for these membrane translocation events. To address this question, Sommer et al. screened the nucleomorph genome of the chromalveolate cryptophyte Guillardia theta (which, similar to P. falciparum, contains a four-membrane-bound plastid organelle) for genes encoding potential translocon-related proteins (49). Surprisingly, the authors identified genes encoding proteins usually involved in the ER-associated protein degradation pathway (ERAD), which recognizes incorrectly folded protein substrates and retrotranslocates them to the cell cytosol for degradation by the ubiquitin (Ub)-proteasome system (35, 44). As such, the ERAD system functions as a translocation complex, capable of transporting proteins across a biological membrane. Further characterization of one of these proteins (G. theta Der1-1, a homologue of yeast Der1p, a component of the ERAD system) provided strong evidence for a plastid localization. These data suggested an attractive solution to the mechanistic problem of transport across the second and third outermost membrane of complex plastids by hypothesizing a role for an ERAD-derived protein translocon complex. Intriguingly, this study also identified several members of this ERAD-derived translocon complex (apicoplast ERAD [apERAD]) in the nuclear genome of P. falciparum endowed with an N-terminal BTS (49). The BTS derived from one of these proteins, P. falciparum sDer1-1 [PfsDer1-1], was sufficient to direct transport of green fluorescent protein (GFP) to the apicoplast of P. falciparum, suggesting that this ERAD-like machinery is ubiquitous among chromalveolates with four membrane-bound plastids (49). In this current report we extend our study of the P. falciparum apERAD complex.     

Distance to the Scaling Law: A Useful Approach for Unveiling Relationships between Crime and Urban Metrics

We report on a quantitative analysis of relationships between the number of homicides, population size and ten other urban metrics. By using data from Brazilian cities, we show that well-defined average scaling laws with the population size emerge when investigating the relations between population and number of homicides as well as population and urban metrics. We also show that the fluctuations around the scaling laws are log-normally distributed, which enabled us to model these scaling laws by a stochastic-like equation driven by a multiplicative and log-normally distributed noise. Because of the scaling laws, we argue that it is better to employ logarithms in order to describe the number of homicides in function of the urban metrics via regression analysis. In addition to the regression analysis, we propose an approach to correlate crime and urban metrics via the evaluation of the distance between the actual value of the number of homicides (as well as the value of the urban metrics) and the value that is expected by the scaling law with the population size. This approach has proved to be robust and useful for unveiling relationships/behaviors that were not properly carried out by the regression analysis, such as the non-explanatory potential of the elderly population when the number of homicides is much above or much below the scaling law, the fact that unemployment has explanatory potential only when the number of homicides is considerably larger than the expected by the power law, and a gender difference in number of homicides, where cities with female population below the scaling law are characterized by a number of homicides above the power law.